From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 20 Jul 2012 21:41:15 +0000 (+0000)
Subject: linkers!
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3614bbf79718eed5617ff8d0072bf2aa047e0209;p=jalview.git

linkers!
---

diff --git a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb
index 564e451..c97c0de 100644
--- a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb
@@ -150,10 +150,14 @@ module Evoruby
         puts( "Mapping file               : " + mapping_file )
         log << "Mapping file               : " + mapping_file + ld
       end
-      if ( extension > 0 )
+      if extension > 0
         puts( "Extension                  : " + extension.to_s )
         log << "Extension                  : " + extension.to_s + ld
       end
+      if extract_linkers
+        puts( "Extract linkers            : true" )
+        log << "Extract linkers            : true" + ld
+      end
       log << "Date                       : " + Time.now.to_s + ld
       puts
 
@@ -237,9 +241,9 @@ module Evoruby
       new_msa_domains_extended = Msa.new
       per_species_counter = 0
       linkers = ""
-      
+
       puts basename
-      
+
       File.open( input_file ) do | file |
         while line = file.gets
           line.strip!
@@ -436,7 +440,7 @@ module Evoruby
       rescue Exception => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
       end
-      
+
       if extract_linkers
         begin
           f = File.open( out_dir + Constants::FILE_SEPARATOR + basename +  LINKERS_SUFFIX , 'a' )
@@ -446,7 +450,7 @@ module Evoruby
           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
         end
       end
-      
+
 
     end